BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708590.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 5,194,549 number of mapped reads = 5,064,096 (97.49%) number of supplementary alignments = 137 (0%) number of secondary alignments = 0 number of mapped bases = 252,584,476 bp number of sequenced bases = 252,562,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,557 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7267 >>>>>>> ACTG content number of A's = 78,558,386 bp (31.1%) number of C's = 47,619,518 bp (18.85%) number of T's = 78,130,850 bp (30.94%) number of G's = 48,245,875 bp (19.1%) number of N's = 7,970 bp (0%) GC percentage = 37.96% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 375,186 number of insertions = 15,923 mapped reads with insertion percentage = 0.31% number of deletions = 12,881 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 0.0816X std coverageData = 0.3063X There is a 7.46% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 19732651 0.07916791108014933 0.29861094063201304 chr2 243199373 22753557 0.09355927492461093 0.3794812796084889 chr3 198022430 18832841 0.0951045848695019 0.32761865923965744 chr4 191154276 19068488 0.09975444127653205 0.3300577151933673 chr5 180915260 17473052 0.09658141607291723 0.3247914219868507 chr6 171115067 17028083 0.0995124701672238 0.33065719920402614 chr7 159138663 14354814 0.09020318337097001 0.31534280657318414 chr8 146364022 13758319 0.0940006895956986 0.32103244254902286 chr9 141213431 10310759 0.07301542726484707 0.2846531005358066 chr10 135534747 10346094 0.07633536217837925 0.2884169546704943 chr11 135006516 11858174 0.08783408646735244 0.31319751569306614 chr12 133851895 12313644 0.09199454367082363 0.32000369837845005 chr13 115169878 10232952 0.08885094069475354 0.31430067912064996 chr14 107349540 7665486 0.07140678944688537 0.2819008637160596 chr15 102531392 6659418 0.06495003988632087 0.2693075026492026 chr16 90354753 4593675 0.05084043558837464 0.23601426583345236 chr17 81195210 3982498 0.0490484352463649 0.23265136866965191 chr18 78077248 7218972 0.09245935512481178 0.31796943854057097 chr19 59128983 1929800 0.03263712484282032 0.1874495093006017 chr20 63025520 3715730 0.058955959427228845 0.25543990046010295 chr21 48129895 3152298 0.06549563426223971 0.27247793005238896 chr22 51304566 1256948 0.02449972971216636 0.16301267370532932 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 14004176 0.09019208792703523 0.31430267870204115 chrY 59373566 341897 0.005758404337714868 0.07999483768305839